Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.


Journal

Chemical science
ISSN: 2041-6520
Titre abrégé: Chem Sci
Pays: England
ID NLM: 101545951

Informations de publication

Date de publication:
28 Jan 2021
Historique:
received: 07 09 2020
accepted: 25 11 2020
entrez: 31 3 2022
pubmed: 26 11 2020
medline: 26 11 2020
Statut: epublish

Résumé

The main protease (M

Identifiants

pubmed: 35356437
doi: 10.1039/d0sc04942e
pii: d0sc04942e
pmc: PMC8899719
doi:

Types de publication

Journal Article

Langues

eng

Pagination

1513-1527

Subventions

Organisme : NIAID NIH HHS
ID : R01 AI148740
Pays : United States

Commentaires et corrections

Type : UpdateOf

Informations de copyright

This journal is © The Royal Society of Chemistry.

Déclaration de conflit d'intérêts

There are no conflicts to declare.

Références

FEBS J. 2014 Sep;281(18):4085-96
pubmed: 25039866
J Phys Chem Lett. 2020 Aug 6;11(15):6262-6265
pubmed: 32658489
Curr Opin Struct Biol. 2020 Oct;64:79-87
pubmed: 32683247
J Comput Chem. 2005 Dec;26(16):1781-802
pubmed: 16222654
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
Science. 2020 Apr 24;368(6489):409-412
pubmed: 32198291
J Virol. 2008 Mar;82(5):2515-27
pubmed: 18094151
Biochemistry. 2004 Apr 20;43(15):4568-74
pubmed: 15078103
Science. 2020 Jun 19;368(6497):1331-1335
pubmed: 32321856
J Chem Inf Model. 2020 Nov 23;60(11):5563-5579
pubmed: 32539374
J Chem Phys. 2020 Sep 21;153(11):115101
pubmed: 32962355
Biochim Biophys Acta Proteins Proteom. 2017 Nov;1865(11 Pt B):1664-1675
pubmed: 28528876
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
J Comput Chem. 2013 Dec 15;34(32):2757-70
pubmed: 24000174
J Comput Aided Mol Des. 2013 Mar;27(3):221-34
pubmed: 23579614
Cell Res. 2020 Aug;30(8):678-692
pubmed: 32541865
J Comput Chem. 2010 Mar;31(4):671-90
pubmed: 19575467
J Struct Biol. 2020 Nov 1;212(2):107617
pubmed: 32919067
Sci Adv. 2018 Apr 04;4(4):eaas8667
pubmed: 29632894
J Chem Theory Comput. 2016 Nov 8;12(11):5411-5421
pubmed: 27709966
Nat Commun. 2020 Jun 24;11(1):3202
pubmed: 32581217
J Mol Biol. 2010 Apr 30;398(2):276-91
pubmed: 20230836
J Biomol Struct Dyn. 2021 May 24;:1-19
pubmed: 34029506
Biophys J. 2007 Feb 15;92(4):1374-83
pubmed: 17142288
J Chem Inf Model. 2012 Dec 21;52(12):3144-54
pubmed: 23146088
J Am Chem Soc. 2002 Nov 6;124(44):13257-64
pubmed: 12405854
Science. 1989 Jun 2;244(4908):1069-72
pubmed: 2727695
Chem Phys Lett. 2020 Jul;750:137489
pubmed: 32313296
J Chem Theory Comput. 2008 Jan;4(1):116-22
pubmed: 26619985
J Chem Inf Model. 2020 Nov 23;60(11):5301-5307
pubmed: 32805108
Bioinformatics. 2015 May 1;31(9):1478-80
pubmed: 25505095
J Biomol Struct Dyn. 2021 Aug;39(12):4522-4535
pubmed: 32552534
J Mol Biol. 2007 Aug 24;371(4):1060-74
pubmed: 17599357
J Comput Aided Mol Des. 2013 Mar;27(3):235-46
pubmed: 23579613
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13190-5
pubmed: 14585926
J Biol Chem. 2006 May 19;281(20):13894-8
pubmed: 16565086
J Med Chem. 2020 May 14;63(9):4562-4578
pubmed: 32045235
Bioorg Med Chem Lett. 2020 Sep 1;30(17):127377
pubmed: 32738988
J Biol Chem. 2005 Jun 17;280(24):22741-8
pubmed: 15831489
Int J Mol Sci. 2020 May 21;21(10):
pubmed: 32455534
Chem Sci. 2020 Jun 25;11(39):10626-10630
pubmed: 34094317
J Chem Inf Model. 2020 Dec 28;60(12):5815-5831
pubmed: 32678588
J Mol Biol. 2005 Nov 18;354(1):25-40
pubmed: 16242152
J Phys Chem B. 2010 Aug 19;114(32):10235-53
pubmed: 20701361
Proteins. 2009 Jul;76(1):151-63
pubmed: 19089987
PLoS One. 2010 Oct 06;5(10):e13197
pubmed: 20949131
Nat Commun. 2017 Oct 16;8(1):955
pubmed: 29038582
Sci Adv. 2019 Mar 20;5(3):eaav0482
pubmed: 30906862
Nature. 2020 Jun;582(7811):289-293
pubmed: 32272481
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W537-41
pubmed: 22570416
Nat Rev Drug Discov. 2017 Dec;16(12):829-842
pubmed: 29075003
Handb Exp Pharmacol. 2009;(189):85-110
pubmed: 19048198
Int J Mol Sci. 2020 Apr 28;21(9):
pubmed: 32353978
J Chem Inf Model. 2020 Dec 28;60(12):5754-5770
pubmed: 32551639
Proc Natl Acad Sci U S A. 1981 May;78(5):2853-5
pubmed: 6265917
J Med Chem. 2016 Jul 28;59(14):6595-628
pubmed: 26878082
Biophys J. 2010 Apr 7;98(7):1327-36
pubmed: 20371333
Nat Methods. 2017 Jan;14(1):71-73
pubmed: 27819658
J Chem Theory Comput. 2011 Feb 8;7(2):525-37
pubmed: 26596171
J Chem Inf Model. 2012 Dec 21;52(12):3155-68
pubmed: 23145473
Biochem Biophys Res Commun. 1967 Apr 20;27(2):157-62
pubmed: 6035483
J Biol Chem. 2020 Dec 11;295(50):17365-17373
pubmed: 33060199
Nat Commun. 2020 Oct 7;11(1):5047
pubmed: 33028810
Biochemistry. 2014 Sep 23;53(37):5930-46
pubmed: 25196915

Auteurs

Anna Pavlova (A)

School of Physics, Georgia Institute of Technology Atlanta GA 30332 USA gumbart@physics.gatech.edu.

Diane L Lynch (DL)

School of Physics, Georgia Institute of Technology Atlanta GA 30332 USA gumbart@physics.gatech.edu.

Isabella Daidone (I)

Department of Physical and Chemical Sciences, University of L'Aquila I-67010 L'Aquila Italy.

Laura Zanetti-Polzi (L)

CNR Institute of Nanoscience I-41125 Modena Italy.

Micholas Dean Smith (MD)

Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville TN 37996 USA.

Chris Chipot (C)

Université de Lorraine, UMR 7019, Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign Vandoeuvre-lès-Nancy F-54500 France.
Department of Physics, University of Illinois at Urbana-Champaign 1110 West Green Street Urbana IL 61801 USA.

Daniel W Kneller (DW)

Neutron Scattering Division, Oak Ridge National Laboratory 1 Bethel Valley Rd Oak Ridge TN 37831 USA.

Andrey Kovalevsky (A)

Neutron Scattering Division, Oak Ridge National Laboratory 1 Bethel Valley Rd Oak Ridge TN 37831 USA.

Leighton Coates (L)

Neutron Scattering Division, Oak Ridge National Laboratory 1 Bethel Valley Rd Oak Ridge TN 37831 USA.

Andrei A Golosov (AA)

Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research 181 Massachusetts Avenue Cambridge Massachusetts 02139 USA.

Callum J Dickson (CJ)

Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research 181 Massachusetts Avenue Cambridge Massachusetts 02139 USA.

Camilo Velez-Vega (C)

Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research 181 Massachusetts Avenue Cambridge Massachusetts 02139 USA.

José S Duca (JS)

Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research 181 Massachusetts Avenue Cambridge Massachusetts 02139 USA.

Josh V Vermaas (JV)

National Center for Computational Sciences, Oak Ridge National Laboratory Oak Ridge TN 37831 USA.

Yui Tik Pang (YT)

School of Physics, Georgia Institute of Technology Atlanta GA 30332 USA gumbart@physics.gatech.edu.

Atanu Acharya (A)

School of Physics, Georgia Institute of Technology Atlanta GA 30332 USA gumbart@physics.gatech.edu.

Jerry M Parks (JM)

UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory TN 37831 USA.

Jeremy C Smith (JC)

Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville TN 37996 USA.
UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory TN 37831 USA.

James C Gumbart (JC)

School of Physics, Georgia Institute of Technology Atlanta GA 30332 USA gumbart@physics.gatech.edu.

Classifications MeSH